ggSmoothExprPlot: ggSmoothExprPlot
In stefanavey/aveytoolkit: Toolkit of Helper Functions

Description Usage Arguments Value Author(s) See Also Examples

View source: R/aveytoolkit_ggSmoothExprPlot.R

Wrapper around ggplot to transform data and plot profiles (e.g. expression or activity) over time

ggSmoothExprPlot(
  x,
  mat,
  rows,
  method = "auto",
  formula = formula("y ~ x"),
  splitRowBy = NA,
  splitColBy = NA,
  colorBy = NULL,
  cols = NA,
  whichCols = NA,
  sep = ".",
  colorByLabel = "Response",
  ggtitle = TRUE,
  xlab = "Time (Days Post-Vaccination)",
  ylab = "Expression",
  colors = c("#1B9E77", "#D95F02", "#7570B3", "#E7298A", "#66A61E", "#E6AB02",
    "#A6761D", "#666666"),
  space = "fixed",
  scales = "fixed",
  fileName = NA,
  plot = TRUE
)

`x`	the numeric x-axis variable for the plot (usually time)
`mat`	data.frame or matrix of values to plot with samples in columns
`rows`	row names or row indices of the items to be plotted
`method`	smoothing method (function). See `stat_smooth`
`formula`	a formula to use for smoothing in `stat_smooth` (e.g. the default "y ~ x" or "y ~ ns(x, 3)").
`splitRowBy`	a factor used to split the data by row in facet_grid
`splitColBy`	a factor used to split the data by col in facet_grid
`colorBy`	a factor used for coloring. No coloring will be done if `NULL` (default)
`cols`	substring to search for with "grep" in column names to be plotted
`whichCols`	the column indices or full column names
`sep`	a separator used in searching for cols in the column names
`colorByLabel`	the labels used for the color legend
`ggtitle`	logical. If TRUE, `rows` is coerced to character and passed to ggtitle
`xlab`	passed to `xlab`. Defaults to "Time (Post-Vaccination)"
`ylab`	passed to `ylab`. Defaults to "Expression"
`colors`	The colors to use. Defaults to the colors given by using RColorBrewer's "Dark2" pallette (but RColorBrewer is not called directly so is not required).
`space`	If `"fixed"`, the default, all panels have the same size. If `"free_y"` their height will be proportional to the length of the y scale; if `"free_x"` their width will be proportional to the length of the x scale; or if `"free"` both height and width will vary. This setting has no effect unless the appropriate scales also vary.
`scales`	Are scales shared across all facets (the default, `"fixed"`), or do they vary across rows (`"free_x"`), columns (`"free_y"`), or both rows and columns (`"free"`)
`fileName`	the name of a file to write a PDF to or `NA` to plot in standard graphics device.
`plot`	logical specifying whether or not to plot the plot(s). Default is TRUE.

invisibly returns a list with 2 elements: ggplot: the ggplot object to be plotted (this can be added to dat: a named list of the data frame(s) passed to data in ggplot. The names come from converting the rows argument to a character vector.

Stefan Avey

ggplot2

data(OrchardSprays)
## Example of functionality
library(Biobase)
data(sample.ExpressionSet, package="Biobase")
dat <- sample.ExpressionSet
## Normally x-axis is time but in this dataset there is no time
## so we will use the `score` as the x-axis
genderF <- dat$sex == "Female"
ggSmoothExprPlot(x=dat$score[genderF],
                 mat=exprs(dat),
                 rows="31345_at",
                 whichCols=which(genderF), # females only
                 colorBy=as.factor(dat$type)[genderF],
                 colorByLabel="Condition",
                 xlab="score")
## Not run: tmp <- ggSmoothExprPlot(x=times[subset], mat=expr, rows=gene,
                                 formula=formula("y ~ ns(x,3)"),
                                 whichCols=subset, colorBy=target[subset,respType],
                                 splitColBy=splitby,
                                 splitRowBy=as.factor(target[subset,"Study"]),
                                 ggtitle=TRUE, colorByLabel=respType, plot=TRUE)
## End(Not run)